You might consider to extend the extensible format to store custom data for your MFT, but wait, you have size limitation here. I am not going to share the exact size, this is something I am leaving for you to figure out 
. By the way, on Windows 8.1 we have reduced this size further. The good news is in near future we will eliminate this restriction from Windows 8.1. I don’t know about Windows 7 though. Anyway, keep an eye on this blog for further update.
So, what can you do to workaround this?
I would suggest you to use a different subtype for your custom format and register your decryptor to handle that format. This may require you to decrypt and decode in the same MFT.